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"Outreach and Training" activities for RBVI annual report and competitive grant renewals
This wiki encompasses all RBVI outreach and training activities, not just those related to Chimera.
The overall goal of the training component of the RBVI is twofold: to improve the general understanding of our technologies in the appropriate population and to create a cadre of biomedical researchers trained in the technology so that they can effectively apply it in their own research.
Each entry below should include the following:
- Title of event (e.g., EMBO electron microscopy workshop)
- Nature of training (e.g., hands-on use of Chimera volume visualization tools)
- Date(s)
- Location
- RBVI staff involved
- Hours of instruction (includes lectures, labs, and prep time)
- Number of attendees
- Comments/remarks/related URLs (e.g., students brought their own data sets for analysis)
2016/2017 report
May 30-June 4, 2016
Faculty at the EMBO Practical Course on Protein-Protein Interactions. A week-long master course funded by the European Molecular Biology Organization held at the Eötvös Loránd University in Budapest, Hungary. Taught sections on Cytoscape as well as Chimera and worked directly with a number of participants on their visualization and analysis challenges. 24 students, 16 hours preparation.
- Scooter Morris
June 5-8, 2016
Pennsylvania State Bioinorganic Workshop. Two 4 hour hands-on workshops on using sequence similarity networks to aid in target selection, analyze metagenomics data, find and explore "linker" sequences, and explore genomic context. Approximately 20 attendees at each workshop. Approximately 1 week preparation + 8 hours teaching.
- Shoshana Brown, Patsy Babbitt
June 6-7, 2016
2 Day Ph.D. course offered at the Eötvös Loránd University in Budapest, Hungary. This was a shortened version of the 6 day course given the week before, but given for credit and pitched to a Ph.D. audience (although faculty were in attendance). Students were required to complete an assignment at the end of the course demonstrating their ability to combine network and structural analyses to investigate biological function. 30 participants, 8 hours preparation.
- Scooter Morris
June 14, 2016
Zika virus Chimera demonstration for 18 San Francisco high school students taking part in the UCSF Public Health Investigators 4 week program. Showed 3d printing, cryoEM and atomic models, protein structure, crawling neutrophils, stereo visualization and oculus rift virtual reality. Two 45 minute demonstrations. 8 hours preparation.
- Tom Goddard
July 29, 2016
Introduction to network visualization and analysis with Cytoscape workshop given at the University of Southern Denmark in Odense, Denmark. 4 hours preparation. Estimated 20 attendees.
- Scooter Morris
August 15-16, 2016
Two day workshop at the University of Colorado, Boulder. Day 1 focused on structural visualization and analysis with UCSF Chimera and day 2 focused on network visualization and analysis with Cytoscape. 20 participants.
- Scooter Morris
September 1-2, 2016
Extended 2 day Cytoscape workshop for the National Cancer Institute on the NIH campus. Total of 24 participants. 16 hours preparation
- Scooter Morris
October 10, 2016
Crawling neutrophil demo, virtual reality vive headset for 14 officers of University of California Extramural Funding Group. Organized by Michael Nordberg at UCSF. 45 minute demonstration, 3 hours preparation.
- Tom Goddard
October 30, 2016
Bay Area Science Festival, white blood cells in virtual reality. Show 6 kids, 5 adults 3d microscopy of crawling cells with stereo projector and Vive VR headset. Showed nuclear pore on Oculus VR headset. Showed CAT lab and EM/NMR facility. 90 minute tour. Organized by Kishore Hari. 8 hours prep (made Oculus / Space Navigator work on Windows).
- Tom Goddard
November 21, 2016
EMBO Conference: Molecular Machines: Integrative Structural and Molecular Biology, Heidelberg. Half-hour talk including ChimeraX demo Visualization and Analysis Challenges of Large Biomolecular Complexes. About 15 hours prep, 100 attendees.
- Tom Ferrin
January 31, 2017
Ribosome antibiotic virtual reality demonstration at Byer's Award reception, Genentech Hall Atrium. Showed 50 visitors antibiotic bound to E coli ribosome and antibiotic resistance mutations during 90 minute reception. Organized by Danica Fujimori. 10 hour preparation and presentation.
- Tom Goddard
February 10 and 17, 2017
Virtual reality demonstration for student applicants to UCSF iPQB program. Showed ribosome antibiotic and crawling neutrophil in collagen filaments. Two demonstrations, 12 students, 30 minutes each. 2 hours preparation. Organized by Rebecca Brown.
- Tom Goddard
March 7, 2017
Tour and virtual reality demonstration for UCSF STEM (science technology engineering and mathematics) Career Day for San Francisco high school students. Showed wet labs and 3d visualization of crawling neutrophil in collagen filaments and E coli ribosome antibiotic. Two tours, 90 minutes and 75 minutes, each with 8 students and 3 adults. 5 hours preparation and presentation. Organized by Jennifer Kaelin.
- Tom Goddard
March 20, 2017
Hands-on training Creating animations with UCSF ChimeraX at the West Coast Protein Crystallography Workshop at Asilomar. Showed how to make spin, morph, density fit, and virtual reality movies. 80 participants, about 50 using ChimeraX on laptop computers. 30 hours preparation and delivery. Organized by Janet Iwasa, Heidi Schubert, Chris Hill.
- Tom Goddard
April 11, 2017
Structural Biology Grid (SBGrid) webinar showing how to use ChimeraX for movie making with cryoEM structures Slides. 40 online participants. Video recorded and available on YouTube at SBGridTV. 20 hours preparation and delivery. Organized by Michelle Ottaviano, Peter Meyer, Jason Key.
- Tom Goddard
June 20-21, 2017
Two antibiotic resistance demonstrations for SF Health Investigators summer program or high school students. Showed macrolide antibiotic resistance by phosphorylation, and ribosome methylation. 20 participants. 5 hours preparation and delivery. Organized by Jenna Bernard, Ben Koo and Rebecca Smith of UCSF Science and Health Education Partnership.
- Tom Goddard
July 19, 2017
Demonstration for 7 legislator staff members for federal and state house and senate members as part of UCSF 101 Day. Visitors included staff for Pelosi, Feinstein, Kamala Harris, Sheehy, Hill, and two others. Discussed clinical and basic research at UCSF. Showed HIV reverse transcriptase with tenofovir inhibitor, E. coli ribosome antibiotic resistance with virtual reality, and molecular playground K-12 education VR software. 3 hours preparation and delivery. Organized by Laura Lane, UCSF associate director for government relations, and Hannah Murphy.
- Alan Brilliant, Tom Goddard
August 1, 2017
Three one-hour hands-on virtual reality demonstrations, each for 7 COSMOS summer high school students from UC Davis. Showed E. coli ribosome antibiotic resistance and molecular playground VR software. Organized by Scooter Morris including other lab tours in the labs of Al Burlingame, Nevan Krogan and Joe DeRisi. 16 hours preparation and delivery.
- Scooter Morris, Alan Brilliant, Tom Goddard
Past reports 2016, 2015, 2014, 2013, 2012, 2011, 2010, 2009, 2008, 2007
